DOCSLIB.ORG

Team Publications UMR3244 – Dynamics of Genetic Information

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Team Publications UMR3244 – Dynamics of Genetic Information Team Publications UMR3244 – Dynamics of Genetic Information Year of publication 2021 Ana Martins Figueiredo, Pedro Barbacena, Ana Russo, Silvia Vaccaro, Daniela Ramalho, Andreia Pena, Aida Pires Lima, Rita Rua Ferreira, Marta Alves Fidalgo, Fatima El-Marjou, Yulia Carvalho, Francisca Ferreira Vasconcelos, Ana-Maria Lennon-Duménil, Danijela Matic Vignjevic, Claudio Areias Franco (2021 Apr 27) Endothelial cell invasion is controlled by dactylopodia. Proceedings of the National Academy of Sciences of the United States of America : DOI : e2023829118 Summary Sprouting angiogenesis is fundamental for development and contributes to cancer, diabetic retinopathy, and cardiovascular diseases. Sprouting angiogenesis depends on the invasive properties of endothelial tip cells. However, there is very limited knowledge on how tip cells invade into tissues. Here, we show that endothelial tip cells use dactylopodia as the main cellular protrusion for invasion into nonvascular extracellular matrix. We show that dactylopodia and filopodia protrusions are balanced by myosin IIA (NMIIA) and actin-related protein 2/3 (Arp2/3) activity. Endothelial cell-autonomous ablation of NMIIA promotes excessive dactylopodia formation in detriment of filopodia. Conversely, endothelial cell- autonomous ablation of Arp2/3 prevents dactylopodia development and leads to excessive filopodia formation. We further show that NMIIA inhibits Rac1-dependent activation of Arp2/3 by regulating the maturation state of focal adhesions. Our discoveries establish a comprehensive model of how endothelial tip cells regulate its protrusive activity and will pave the way toward strategies to block invasive tip cells during sprouting angiogenesis. Shanna L Bowman, Linh Le, Yueyao Zhu, Dawn C Harper, Anand Sitaram, Alexander C Theos, Elena V Sviderskaya, Dorothy C Bennett, Graça Raposo-Benedetti, David J Owen, Megan K Dennis, Michael S Marks (2021 Apr 22) A BLOC-1-AP-3 super-complex sorts a cis-SNARE complex into endosome-derived tubular transport carriers. The Journal of cell biology : DOI : e202005173 Summary Membrane transport carriers fuse with target membranes through engagement of cognate vSNAREs and tSNAREs on each membrane. How vSNAREs are sorted into transport carriers is incompletely understood. Here we show that VAMP7, the vSNARE for fusing endosome- derived tubular transport carriers with maturing melanosomes in melanocytes, is sorted into transport carriers in complex with the tSNARE component STX13. Sorting requires either recognition of VAMP7 by the AP-3δ subunit of AP-3 or of STX13 by the pallidin subunit of BLOC-1, but not both. Consequently, melanocytes expressing both AP-3δ and pallidin variants that cannot bind their respective SNARE proteins are hypopigmented and fail to sort BLOC-1-dependent cargo, STX13, or VAMP7 into transport carriers. However, SNARE binding INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 1 Team Publications UMR3244 – Dynamics of Genetic Information does not influence BLOC-1 function in generating tubular transport carriers. These data reveal a novel mechanism of vSNARE sorting by recognition of redundant sorting determinants on a SNARE complex by an AP-3-BLOC-1 super-complex. Abegão L.M., Santos F.A., Piguel S., Rodrigues J.J., Mendonça C.R., De Boni L. (2021 Apr 15) The ability of 2,5-disubstituted oxazole dyes derivatives to generate two-photon upconversion photoluminescence and its brightness evaluation Journal of Photochemistry and Photobiology A: Chemistry : 411 : 113214 : DOI : 10.1016/j.jphotochem.2021.113214 Summary The brightness study of emissive compounds is one of the fundamental spectroscopic characterizations. In this work, we assessed the brightness values of eight 2,5-disubstituted oxazole dyes derivatives by combining linear and nonlinear spectroscopic parameters. The range of the brightness values obtained is from 0.26 GM to 15.15 GM. The highest value belongs to compound 14 m, which, compared to previously investigated compounds of similar π-conjugation length, is at least two times higher. Brightness values were determined in the spectral region between 700 nm–720 nm, revealing this class of dyes’ potential to be used as photoluminescence bioprobes excited by two-photons. Patrick T Rudak, Joshua Choi, Katie M Parkins, Kelly L Summers, Dwayne N Jackson, Paula J Foster, Anton I Skaro, Ken Leslie, Vivian C McAlister, Vijay K Kuchroo, Wataru Inoue, Olivier Lantz, S M Mansour Haeryfar (2021 Apr 14) INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 2 Team Publications UMR3244 – Dynamics of Genetic Information Chronic stress physically spares but functionally impairs innate-like invariant T cells. Cell reports : 108979 : DOI : S2211-1247(21)00293-X Summary The deleterious effects of psychological stress on mainstream T lymphocytes are well documented. However, how stress impacts innate-like T cells is unclear. We report that long- term stress surprisingly abrogates both T helper 1 (T1)- and T2-type responses orchestrated by invariant natural killer T (iNKT) cells. This is not due to iNKT cell death because these cells are unusually refractory to stress-inflicted apoptosis. Activated iNKT cells in stressed mice exhibit a “split” inflammatory signature and trigger sudden serum interleukin-10 (IL-10), IL-23, and IL-27 spikes. iNKT cell dysregulation is mediated by cell-autonomous glucocorticoid receptor signaling and corrected upon habituation to predictable stressors. Importantly, under stress, iNKT cells fail to potentiate cytotoxicity against lymphoma or to reduce the burden of metastatic melanoma. Finally, stress physically spares mouse mucosa- associated invariant T (MAIT) cells but hinders their T1-/T2-type responses. The above findings are corroborated in human peripheral blood and hepatic iNKT/MAIT cell cultures. Our work uncovers a mechanism of stress-induced immunosuppression. Szuba Agata, Bano Fouzia, Castro Linares Gerard , Iv Francois, Mavrakis Manos*, Richter Ralf P*, Bertin Aurélie*, Koenderink Gijsje H* (2021 Apr 13) Membrane binding controls ordered self-assembly of animal septins eLifeeLife : eLife 2021;10:e63349 : DOI : 10.7554/eLife.63349 Summary Septins are conserved cytoskeletal proteins that regulate cell cortex mechanics. The mechanisms of their interactions with the plasma membrane remain poorly understood. Here we show by cell-free reconstitution that binding to flat lipid membranes requires electrostatic interactions of septins with anionic lipids and promotes the ordered self-assembly of fly septins into filamentous meshworks. Transmission electron microscopy reveals that both fly and mammalian septin hexamers form arrays of single and paired filaments. Atomic force microscopy and quartz crystal microbalance demonstrate that the fly filaments form mechanically rigid, 12 to 18 nm thick, double layers of septins. By contrast, C-terminally truncated septin mutants form 4 nm thin monolayers, indicating that stacking requires the C- terminal coiled coils on DSep2 and Pnut subunits. Our work shows that membrane binding is required for fly septins to form ordered arrays of single and paired filaments and provides new insights into the mechanisms by which septins may regulate cell surface mechanics. Ophélie Lautier, Arianna Penzo, Jérôme O Rouvière, Guillaume Chevreux, Louis Collet, Isabelle Loïodice, Angela Taddei, Frédéric Devaux, Martine A Collart, Benoit Palancade (2021 Apr 10) Co-translational assembly and localized translation of nucleoporins in nuclear INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 3 Team Publications UMR3244 – Dynamics of Genetic Information pore complex biogenesis. Molecular cell : DOI : S1097-2765(21)00225-2 Summary mRNA translation is coupled to multiprotein complex assembly in the cytoplasm or to protein delivery into intracellular compartments. Here, by combining systematic RNA immunoprecipitation and single-molecule RNA imaging in yeast, we have provided a complete depiction of the co-translational events involved in the biogenesis of a large multiprotein assembly, the nuclear pore complex (NPC). We report that binary interactions between NPC subunits can be established during translation, in the cytoplasm. Strikingly, the nucleoporins Nup1/Nup2, together with a number of nuclear proteins, are instead translated at nuclear pores, through a mechanism involving interactions between their nascent N- termini and nuclear transport receptors. Uncoupling this co-translational recruitment further triggers the formation of cytoplasmic foci of unassembled polypeptides. Altogether, our data reveal that distinct, spatially segregated modes of co-translational interactions foster the ordered assembly of NPC subunits and that localized translation can ensure the proper delivery of proteins to the pore and the nucleus. Marion Blin, Laurent Lacroix, Nataliya Petryk, Yan Jaszczyszyn, Chun-Long Chen, Olivier Hyrien, Benoît Le Tallec (2021 Apr 9) DNA molecular combing-based replication fork directionality profiling. Nucleic acids research : DOI : gkab219 Summary The replication strategy of metazoan genomes is still unclear, mainly because definitive maps of replication origins are missing. High-throughput methods are based on population average and thus may exclusively identify efficient initiation sites, whereas inefficient origins go undetected. Single-molecule analyses of specific loci can detect both common and rare initiation events along the targeted regions. However, these usually concentrate on positioning individual events, which only gives an overview of the replication
Load more

Recommended publications
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Transcriptome Sequencing and Genome-Wide Association Analyses Reveal Lysosomal Function and Actin Cytoskeleton Remodeling in Schizophrenia and Bipolar Disorder
    Molecular Psychiatry (2015) 20, 563–572 © 2015 Macmillan Publishers Limited All rights reserved 1359-4184/15 www.nature.com/mp ORIGINAL ARTICLE Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder Z Zhao1,6,JXu2,6, J Chen3,6, S Kim4, M Reimers3, S-A Bacanu3,HYu1, C Liu5, J Sun1, Q Wang1, P Jia1,FXu2, Y Zhang2, KS Kendler3, Z Peng2 and X Chen3 Schizophrenia (SCZ) and bipolar disorder (BPD) are severe mental disorders with high heritability. Clinicians have long noticed the similarities of clinic symptoms between these disorders. In recent years, accumulating evidence indicates some shared genetic liabilities. However, what is shared remains elusive. In this study, we conducted whole transcriptome analysis of post-mortem brain tissues (cingulate cortex) from SCZ, BPD and control subjects, and identified differentially expressed genes in these disorders. We found 105 and 153 genes differentially expressed in SCZ and BPD, respectively. By comparing the t-test scores, we found that many of the genes differentially expressed in SCZ and BPD are concordant in their expression level (q ⩽ 0.01, 53 genes; q ⩽ 0.05, 213 genes; q ⩽ 0.1, 885 genes). Using genome-wide association data from the Psychiatric Genomics Consortium, we found that these differentially and concordantly expressed genes were enriched in association signals for both SCZ (Po10 − 7) and BPD (P = 0.029). To our knowledge, this is the first time that a substantially large number of genes show concordant expression and association for both SCZ and BPD. Pathway analyses of these genes indicated that they are involved in the lysosome, Fc gamma receptor-mediated phagocytosis, regulation of actin cytoskeleton pathways, along with several cancer pathways.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]
  • WNT16 Is a New Marker of Senescence
    Table S1. A. Complete list of 177 genes overexpressed in replicative senescence Value Gene Description UniGene RefSeq 2.440 WNT16 wingless-type MMTV integration site family, member 16 (WNT16), transcript variant 2, mRNA. Hs.272375 NM_016087 2.355 MMP10 matrix metallopeptidase 10 (stromelysin 2) (MMP10), mRNA. Hs.2258 NM_002425 2.344 MMP3 matrix metallopeptidase 3 (stromelysin 1, progelatinase) (MMP3), mRNA. Hs.375129 NM_002422 2.300 HIST1H2AC Histone cluster 1, H2ac Hs.484950 2.134 CLDN1 claudin 1 (CLDN1), mRNA. Hs.439060 NM_021101 2.119 TSPAN13 tetraspanin 13 (TSPAN13), mRNA. Hs.364544 NM_014399 2.112 HIST2H2BE histone cluster 2, H2be (HIST2H2BE), mRNA. Hs.2178 NM_003528 2.070 HIST2H2BE histone cluster 2, H2be (HIST2H2BE), mRNA. Hs.2178 NM_003528 2.026 DCBLD2 discoidin, CUB and LCCL domain containing 2 (DCBLD2), mRNA. Hs.203691 NM_080927 2.007 SERPINB2 serpin peptidase inhibitor, clade B (ovalbumin), member 2 (SERPINB2), mRNA. Hs.594481 NM_002575 2.004 HIST2H2BE histone cluster 2, H2be (HIST2H2BE), mRNA. Hs.2178 NM_003528 1.989 OBFC2A Oligonucleotide/oligosaccharide-binding fold containing 2A Hs.591610 1.962 HIST2H2BE histone cluster 2, H2be (HIST2H2BE), mRNA. Hs.2178 NM_003528 1.947 PLCB4 phospholipase C, beta 4 (PLCB4), transcript variant 2, mRNA. Hs.472101 NM_182797 1.934 PLCB4 phospholipase C, beta 4 (PLCB4), transcript variant 1, mRNA. Hs.472101 NM_000933 1.933 KRTAP1-5 keratin associated protein 1-5 (KRTAP1-5), mRNA. Hs.534499 NM_031957 1.894 HIST2H2BE histone cluster 2, H2be (HIST2H2BE), mRNA. Hs.2178 NM_003528 1.884 CYTL1 cytokine-like 1 (CYTL1), mRNA. Hs.13872 NM_018659 tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain (TNFRSF10D), 1.848 TNFRSF10D Hs.213467 NM_003840 mRNA.
    [Show full text]
  • BUB3 Antibody
    Efficient Professional Protein and Antibody Platforms BUB3 Antibody Basic information: Catalog No.: UPA63666 Source: Rabbit Size: 50ul/100ul Clonality: Monoclonal Concentration: 1mg/ml Isotype: Rabbit IgG Purification: Protein A affinity purified Useful Information: WB:1:500-1:2000 ICC:1:50-1:200 Applications: IHC:1:50-1:200 IP:1:10-1:50 FC:1:50-1:100 Reactivity: Human, Mouse, Rat Specificity: This antibody recognizes BUB3 protein. Immunogen: Recombinant protein corresponding to the N-terminus of human Bub3. BUB3 (budding uninhibited by benzimidazoles 3 homolog), also known as BUB3L or hBUB3, is a conserved component of the mitotic spindle assembly complex (MCC). It contains five WD repeat domains and forms cell cycle constitutive complexes with BUB1 and BUBR1. BUB3 is essential for the ki- netochore localization of BUB1 and BUBR1. As a component of the MCC, BUB3 is involved in the essential spindle checkpoint pathway that operates Description: during early embryogenesis. The spindle checkpoint pathway functions to postpone the initiation of anaphase until chromosomes are properly at- tached to the spindle. This acts to ensure accurate chromosome segrega- tion. In addition, BUB3 plays a role in regulating the establishment of cor- rect kinetochore-microtubule attachments. BUB3 is also thought to bind Tctex1L (or DYNLT3), a dynein light chain. Uniprot: O43684(Human) Q9WVA3(Mouse) BiowMW: 37 kDa Buffer: 1*TBS (pH7.4), 1%BSA, 40%Glycerol. Preservative: 0.05% Sodium Azide. Storage: Store at 4°C short term and -20°C long term. Avoid freeze-thaw cycles. Note: For research use only, not for use in diagnostic procedure. Data: Gene Universal Technology Co.
    [Show full text]
  • 1 Fibrillar Αβ Triggers Microglial Proteome Alterations and Dysfunction in Alzheimer Mouse 1 Models 2 3 4 Laura Sebastian
    bioRxiv preprint doi: https://doi.org/10.1101/861146; this version posted December 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Fibrillar triggers microglial proteome alterations and dysfunction in Alzheimer mouse 2 models 3 4 5 Laura Sebastian Monasor1,10*, Stephan A. Müller1*, Alessio Colombo1, Jasmin König1,2, Stefan 6 Roth3, Arthur Liesz3,4, Anna Berghofer5, Takashi Saito6,7, Takaomi C. Saido6, Jochen Herms1,4,8, 7 Michael Willem9, Christian Haass1,4,9, Stefan F. Lichtenthaler 1,4,5# & Sabina Tahirovic1# 8 9 1 German Center for Neurodegenerative Diseases (DZNE) Munich, 81377 Munich, Germany 10 2 Faculty of Chemistry, Technical University of Munich, Garching, Germany 11 3 Institute for Stroke and Dementia Research (ISD), Ludwig-Maximilians Universität München, 12 81377 Munich, Germany 13 4 Munich Cluster for Systems Neurology (SyNergy), Munich, Germany 14 5 Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 15 Munich, Germany 16 6 Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science Institute, Wako, 17 Saitama 351-0198, Japan 18 7 Department of Neurocognitive Science, Nagoya City University Graduate School of Medical 19 Science, Nagoya, Aichi 467-8601, Japan 20 8 Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität München, 81377 21 Munich, Germany 22 9 Biomedical Center (BMC), Ludwig-Maximilians Universität München, 81377 Munich, Germany 23 10 Graduate School of Systemic Neuroscience, Ludwig-Maximilians-University Munich, Munich, 24 Germany. 25 *Contributed equally 26 #Correspondence: [email protected] and [email protected] 27 28 Running title: 29 Microglial proteomic signatures of AD 30 Keywords: Alzheimer’s disease / microglia / proteomic signatures / neuroinflammation / 31 phagocytosis 32 1 bioRxiv preprint doi: https://doi.org/10.1101/861146; this version posted December 2, 2019.
    [Show full text]
  • Supplementary Dataset S2
    mitochondrial translational termination MRPL28 MRPS26 6 MRPS21 PTCD3 MTRF1L 4 MRPL50 MRPS18A MRPS17 2 MRPL20 MRPL52 0 MRPL17 MRPS33 MRPS15 −2 MRPL45 MRPL30 MRPS27 AURKAIP1 MRPL18 MRPL3 MRPS6 MRPS18B MRPL41 MRPS2 MRPL34 GADD45GIP1 ERAL1 MRPL37 MRPS10 MRPL42 MRPL19 MRPS35 MRPL9 MRPL24 MRPS5 MRPL44 MRPS23 MRPS25 ITB ITB ITB ITB ICa ICr ITL original ICr ICa ITL ICa ITL original ICr ITL ICr ICa mitochondrial translational elongation MRPL28 MRPS26 6 MRPS21 PTCD3 MRPS18A 4 MRPS17 MRPL20 2 MRPS15 MRPL45 MRPL52 0 MRPS33 MRPL30 −2 MRPS27 AURKAIP1 MRPS10 MRPL42 MRPL19 MRPL18 MRPL3 MRPS6 MRPL24 MRPS35 MRPL9 MRPS18B MRPL41 MRPS2 MRPL34 MRPS5 MRPL44 MRPS23 MRPS25 MRPL50 MRPL17 GADD45GIP1 ERAL1 MRPL37 ITB ITB ITB ITB ICa ICr original ICr ITL ICa ITL ICa ITL original ICr ITL ICr ICa translational termination MRPL28 MRPS26 6 MRPS21 PTCD3 C12orf65 4 MTRF1L MRPL50 MRPS18A 2 MRPS17 MRPL20 0 MRPL52 MRPL17 MRPS33 −2 MRPS15 MRPL45 MRPL30 MRPS27 AURKAIP1 MRPL18 MRPL3 MRPS6 MRPS18B MRPL41 MRPS2 MRPL34 GADD45GIP1 ERAL1 MRPL37 MRPS10 MRPL42 MRPL19 MRPS35 MRPL9 MRPL24 MRPS5 MRPL44 MRPS23 MRPS25 ITB ITB ITB ITB ICa ICr original ICr ITL ICa ITL ICa ITL original ICr ITL ICr ICa translational elongation DIO2 MRPS18B MRPL41 6 MRPS2 MRPL34 GADD45GIP1 4 ERAL1 MRPL37 2 MRPS10 MRPL42 MRPL19 0 MRPL30 MRPS27 AURKAIP1 −2 MRPL18 MRPL3 MRPS6 MRPS35 MRPL9 EEF2K MRPL50 MRPS5 MRPL44 MRPS23 MRPS25 MRPL24 MRPS33 MRPL52 EIF5A2 MRPL17 SECISBP2 MRPS15 MRPL45 MRPS18A MRPS17 MRPL20 MRPL28 MRPS26 MRPS21 PTCD3 ITB ITB ITB ITB ICa ICr ICr ITL original ITL ICa ICa ITL ICr ICr ICa original
    [Show full text]
  • Team Publications Structure and Membrane Compartments
    Team Publications Structure and membrane compartments Year of publication 2021 Graça Raposo, Guillaume van Niel, Philip D Stahl (2021 Jun 14) Extracellular vesicles and homeostasis-An emerging field in bioscience research. FASEB bioAdvances : 456-458 : DOI : 10.1096/fba.2021-00009 Summary To keep abreast of developments in the biological sciences and in parallel fields such as medical education, () has created a special collections category, special collections ( SC), that target, among other topics, emerging disciplines in the biomedical sciences. This SC is focused on the emerging field of extracellular vesicles (EVs) and homeostasis. Leading investigators in the biology of EVs around the globe have contributed to this collection of articles that cover the gamut of research activities from biogenesis and secretion to physiological function. Silvia Benito-Martinez, Laura Salavessa, Graça Raposo, Michael S Marks, Cédric Delevoye (2021 May 22) Melanin transfer and fate within keratinocytes in human skin pigmentation. Integrative and comparative biology : DOI : icab094 Summary Human skin and hair pigmentation play important roles in social behavior but also in photoprotection from the harmful effects of ultraviolet light. The main pigments in mammalian skin, the melanins, are synthesized within specialized organelles called melanosomes in melanocytes, which sit at the basal layer of the epidermis and the hair bulb. The melanins are then transferred from melanocytes to keratinocytes, where they accumulate perinuclearly in membrane-bound organelles as a “cap” above the nucleus. The mechanism of transfer, the nature of the pigmented organelles within keratinocytes, and the mechanism governing their intracellular positioning are all debated and poorly understood, but likely play an important role in the photoprotective properties of melanin in the skin.
    [Show full text]
  • Control of the Physical and Antimicrobial Skin Barrier by an IL-31–IL-1 Signaling Network
    The Journal of Immunology Control of the Physical and Antimicrobial Skin Barrier by an IL-31–IL-1 Signaling Network Kai H. Ha¨nel,*,†,1,2 Carolina M. Pfaff,*,†,1 Christian Cornelissen,*,†,3 Philipp M. Amann,*,4 Yvonne Marquardt,* Katharina Czaja,* Arianna Kim,‡ Bernhard Luscher,€ †,5 and Jens M. Baron*,5 Atopic dermatitis, a chronic inflammatory skin disease with increasing prevalence, is closely associated with skin barrier defects. A cy- tokine related to disease severity and inhibition of keratinocyte differentiation is IL-31. To identify its molecular targets, IL-31–dependent gene expression was determined in three-dimensional organotypic skin models. IL-31–regulated genes are involved in the formation of an intact physical skin barrier. Many of these genes were poorly induced during differentiation as a consequence of IL-31 treatment, resulting in increased penetrability to allergens and irritants. Furthermore, studies employing cell-sorted skin equivalents in SCID/NOD mice demonstrated enhanced transepidermal water loss following s.c. administration of IL-31. We identified the IL-1 cytokine network as a downstream effector of IL-31 signaling. Anakinra, an IL-1R antagonist, blocked the IL-31 effects on skin differentiation. In addition to the effects on the physical barrier, IL-31 stimulated the expression of antimicrobial peptides, thereby inhibiting bacterial growth on the three-dimensional organotypic skin models. This was evident already at low doses of IL-31, insufficient to interfere with the physical barrier. Together, these findings demonstrate that IL-31 affects keratinocyte differentiation in multiple ways and that the IL-1 cytokine network is a major downstream effector of IL-31 signaling in deregulating the physical skin barrier.
    [Show full text]
  • SUPPORTING INFORMATION for Regulation of Gene Expression By
    SUPPORTING INFORMATION for Regulation of gene expression by the BLM helicase correlates with the presence of G4 motifs Giang Huong Nguyen1,2, Weiliang Tang3, Ana I. Robles1, Richard P. Beyer4, Lucas T. Gray5, Judith A. Welsh1, Aaron J. Schetter1, Kensuke Kumamoto1,6, Xin Wei Wang1, Ian D. Hickson2,7, Nancy Maizels5, 3,8 1 Raymond J. Monnat, Jr. and Curtis C. Harris 1Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, U.S.A; 2Department of Medical Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, U.K.; 3Department of Pathology, University of Washington, Seattle, WA U.S.A.; 4 Center for Ecogenetics and Environmental Health, University of Washington, Seattle, WA U.S.A.; 5Department of Immunology and Department of Biochemistry, University of Washington, Seattle, WA U.S.A.; 6Department of Organ Regulatory Surgery, Fukushima Medical University, Fukushima, Japan; 7Cellular and Molecular Medicine, Nordea Center for Healthy Aging, University of Copenhagen, Denmark; 8Department of Genome Sciences, University of WA, Seattle, WA U.S.A. SI Index: Supporting Information for this manuscript includes the following 19 items. A more detailed Materials and Methods section is followed by 18 Tables and Figures in order of their appearance in the manuscript text: 1) SI Materials and Methods 2) Figure S1. Study design and experimental workflow. 3) Figure S2. Immunoblot verification of BLM depletion from human fibroblasts. 4) Figure S3. PCA of mRNA and miRNA expression in BLM-depleted human fibroblasts. 5) Figure S4. qPCR confirmation of mRNA array data. 6) Table S1. BS patient and control detail.
    [Show full text]
  • Supplemental Figures
    Supplemental Figures Supplementary Fig 1. External validation of GSTO1 with patient survival and relation of GSTO1 expression to tumor stages and grades. A, External validation of GSTO1 with patient survival using Rembrandt and Gravendeel Glioma data sets. B, GSTO1 expression is higher in GBM compared to LGG in TCGA data sets. C, GSTO1 expression increases in KIRC is significantly different between tumor stages and grades. Supplementary Fig 2. Validation of GSTO1 knockout A, Western blot probing GSTO1 in nt WT and GSTO1 KO cells after 10, 20, 30 passages. B, Reverse transcriptional real time PCR detection of GSTO1 in nt WT and GSTO1 KO single clones. C, Sanger sequence of GSTO1 KO cell lines Supplementary Fig 3. 3-dimension spheroids of (A) HCT116 nt WT and GSTO1 cells, (B) U-87 MG nt WT and GSTO1 cells Supplementary Fig 4. Neurospheroid formation of U-87 MG nt WT and GSTO1 KO single clones. Supplementary Fig 5. Genes and gene sets up- or down-regulated in U-87 MG, HCT116 and A172 as a result of GSTO1 KO in Bru-seq. A, Genes up- or down- regulated in U-87 MG, HCT116 and A172 as a result of GSTO1 KO. B, Top 10 significant enrichment gene sets modulated by GSTO1 KO in enrichment analysis (GSEA). Supplementary Fig 6. GSEA plots for highlighted significantly changed gene sets. A, GSEA plots for common significantly changed gene sets overlapped in nascent (Bru- seq) transcriptomic profiles between HCT116 and U-87 MG cells in response to GSTO1 KO. B, GSEA plots for UV response gene sets in nascent (Bru-seq) transcriptomic profiles in U-87 MG GSTO1 KO cells.
    [Show full text]